SoilR: Models of Soil Organic Matter Decomposition

SoilR is a modeling framework that contains a library of functions and tools for modeling soil organic matter decomposition under the R environment for computing (Sierra, Müller, & Trumbore, 2012; Sierra, Müller, & Trumbore, 2014). It implements a variety of model structures and tools to represent carbon storage and release from soil organic matter. In SoilR, organic matter decomposition is represented as a non-linear system of ordinary differential equations that generalizes the structure of most compartment-based decomposition models.

You can obtain the latest version of SoilR from our GitHub repository . To install, follow the instructions on the Workflow below about first steps.

SoilR Workflows

In this site you will find useful information on how to run SoilR and perform analyses useful for your research. Each Workflow is writen in the form of blogpost and contains different examples for performing different analyses with SoilR. You can ask questions using the commenting platform and get feedback from a larger community.

Workflows by date
Nonlinear microbial explicit models
Temperature and moisture modifiers
Bind pre-, post-bomb, and forecast atmospheric radiocarbon curves
Multiple-pool radiocarbon models
Ages and transit times in linear models
Introduction to radiocarbon models
Identify kinetic SOM fractions with incubation data
Run the RothC model for a site
Run multiple-pool models
Olson's 1963 model
Run a one-pool model
First steps with R and SoilR

Training

Occasionally, we offer training on how to use SoilR at conferences or workshops. The last SoilR workshop took place between October 10th-14th, 2016, at the Max Planck Institute for Biogeochemistry.

References

  1. Sierra, C. A., Müller, M., & Trumbore, S. E. (2014). Modeling radiocarbon dynamics in soils: SoilR version 1.1. Geoscientific Model Development, 7(5), 1919–1931. doi:10.5194/gmd-7-1919-2014
  2. Sierra, C. A., Müller, M., & Trumbore, S. E. (2012). Models of soil organic matter decomposition: the SoilR package, version 1.0. Geosci. Model Dev., 5(4), 1045–1060. doi:10.5194/gmd-5-1045-2012